| translate {Biostrings} | R Documentation |
Functions for transcription and/or translation of DNA or RNA sequences, and related utilities.
transcribe(x) cDNA(x) codons(x) translate(x) ## Related utilities dna2rna(x) rna2dna(x)
x |
A DNAString object for transcribe and dna2rna.
An RNAString object for cDNA and rna2dna.
A DNAString, RNAString, MaskedDNAString or MaskedRNAString object for codons.
A DNAString, RNAString, DNAStringSet, RNAStringSet, MaskedDNAString or MaskedRNAString object for translate.
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transcribe reproduces the biological process of DNA
transcription that occurs in the cell.
cDNA reproduces the process of synthesizing complementary DNA
from a mature mRNA template.
translate reproduces the biological process of RNA
translation that occurs in the cell.
The input of the function can be either RNA or coding DNA.
The Standard Genetic Code (see ?GENETIC_CODE) is
used to translate codons into amino acids.
codons is a utility for extracting the codons involved
in this translation without translating them.
dna2rna and rna2dna are low-level utilities for
converting sequences from DNA to RNA and vice-versa.
All what this converstion does is to replace each occurence of T
by a U and vice-versa.
An RNAString object for transcribe and dna2rna.
A DNAString object for cDNA and rna2dna.
Note that if the sequence passed to transcribe or cDNA
is considered to be oriented 5'-3', then the returned sequence is
oriented 3'-5'.
An XStringViews object with 1 view per codon for codons.
When x is a MaskedDNAString or MaskedRNAString
object, its masked parts are interpreted as introns and filled with
the + letter in the returned object. Therefore codons that span across
masked regions are represented by views that have a width > 3 and
contain the + letter. Note that each view is guaranteed to contain
exactly 3 base letters.
An AAString object for translate.
reverseComplement,
GENETIC_CODE,
DNAString-class,
RNAString-class,
AAString-class,
XStringSet-class,
XStringViews-class,
MaskedXString-class
file <- system.file("extdata", "someORF.fa", package="Biostrings")
x <- read.DNAStringSet(file, "fasta")
x
## The first and last 1000 nucleotides are not part of the ORFs:
x <- DNAStringSet(x, start=1001, end=-1001)
## Before calling translate() on an ORF, we need to mask the introns
## if any. We can get this information fron the SGD database
## (http://www.yeastgenome.org/).
## According to SGD, the 1st ORF (YAL001C) has an intron at 71..160
## (see http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YAL001C)
y1 <- x[[1]]
mask1 <- Mask(length(y1), start=71, end=160)
masks(y1) <- mask1
y1
translate(y1)
## Codons
codons(y1)
which(width(codons(y1)) != 3)
codons(y1)[20:28]